Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 15248 b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Keio:15248 Length = 378 Score = 225 bits (574), Expect = 1e-63 Identities = 134/306 (43%), Positives = 185/306 (60%), Gaps = 27/306 (8%) Query: 4 IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63 +QL + K F + L L I++ EFL L+GPSGCGK+T LR++AGLET SG I + Sbjct: 18 VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77 Query: 64 GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLG 123 + + + +NR + VFQ YAL+PHMTV +N+ FGL ++ +AE RV+E + Sbjct: 78 NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKT-PAAEITPRVMEALRMVQ 136 Query: 124 IADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQ 183 + RKP +LSGGQQQRVA+ RA+V P + L+DE LS LD KLR +M+ EL+ LQ + Sbjct: 137 LETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRK 196 Query: 184 LAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINLV 243 L +T V+VTH+Q EA+TM+DRI VM DG ++Q +P E Y EP NLFVA FIGE IN+ Sbjct: 197 LGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGE--INMF 254 Query: 244 RGTRSESTFVGEHFSYPLDED-VMESVDDRD-----DFVLG--------VRPEDIEVADA 289 T E LDE V +V+ R+ +F + +RPED+ V + Sbjct: 255 NATVIER----------LDEQRVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRVEEI 304 Query: 290 APDDAA 295 D+ A Sbjct: 305 NDDNHA 310 Lambda K H 0.317 0.135 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 349 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 383 Length of database: 378 Length adjustment: 30 Effective length of query: 353 Effective length of database: 348 Effective search space: 122844 Effective search space used: 122844 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory